Rheumatoid arthritis (RA) is a chronic disease affecting 1% of US adults. Because of high morbidity and mortality of RA, identification of effective treatment is of great importance. Methotrexate is considered the gold-standard treatment for RA; however, there is large between-person variation in response to MTX, such that it is ineffective in 30-40% of treated individuals. Although not extensively studied, early reports demonstrate that genetic variation contributes to inconsistent MTX efficacy and toxicity. We propose to use a comprehensive candidate gene approach to characterize loci that determine efficacy and toxicity of MTX used to treat RA. We will build on the expertise of a multidisciplinary team of investigators within a large clinical trial, Treatment of Early Aggressive RA (TEAR), to study the pharmacogenetics of MTX in RA. TEAR is a Phase IV, investigator-initiated trial enrolling 750 treatment-naive RA patients. All patients will be treated with MTX with doses uptitrated to 20 mg/wk within 12 wks of study entry. For this proposal, we will focus on the first 24 wk of the trial since those who are genetically susceptible to MTX efficacy or toxicity will likely express these treatment-related phenotypes early. DMA has been isolated for 95% of enrolled subjects; we will evaluate 641 subjects. To accomplish our first aim we will characterize the association between genetic variation and MTX efficacy and toxicity using the following steps: (1) Select and genotype all haplotypetagging SNPs or genetic variants reported to be related to the efficacy or toxicity of MTX in 26 candidate genes regulating transporters, glutamination enzymes, and folate and purine metabolism. (2) Analyze single variants and haplotypes to assess associations between genetic variation and (a) efficacy (via the longitudinal change in a clinical index calculated as a function of the number of tender joints, CRP concentration, and patients' assessment of disease along a 10 cm visual scale, measured at baseline and 12-wk intervals); (b) MTX polyglutamate concentrations (which enhances intracellular retention of MTX and causes an anti-proliferative effect and the release of the anti-inflammatory, adenosine), and (c) toxicity (gastrointestinal, mucocutaneous, hematopoietic, or renal adverse effects during the first 24 wks). We will use linear regression models to evaluate main effects of genetic variants as well as gene-gene interaction and to control for confounding by other drugs. We will use structured association testing to control for confounding by ancestral history. To accomplish our second aim, we will evaluate the role of non-genetic factors (baseline CRP, RF, and anti-CCP antibody status) that mediate effects of genetic variants identified in Aim 1. We anticipate that characterization of genetic predictors of efficacy and toxicity of MTX will improve our ability to personalize treatment by targeting the 60-70% who are MTX responsive and reducing the trial and error approach of treating 100% of RA patients with a drug that is harmful to at least 10%.